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This study focuses on the geochemical features of the presently discharging thermal and cold springs and on paleofluids from the upstream portion of the Reno river basin (Alto Reno; central–northern Italy). The aim is investigating the primary sources of the modern and fossil fluids and the interactions between deep and shallow aquifers. Paleofluids are from fluid inclusions hosted within euhedral and hopper quartz crystals and consist of a two-phase, liquid–vapor aqueous fluid and a unary CH4 fluid. The aqueous inclusions have constant phase ratios and a calculated salinity of ~ 1.5 wt% NaCleq. They homogenize by bubble disappearance at 100–200 °C, whereas the estimated entrapment depth is ~ 3–5.5 km. The paleofluids likely represent the vestiges of the deep and hot, CH4-rich, Na+–Cl− fluids produced by the interaction between meteoric waters and Triassic and Miocene formations. The modern Na+–Cl−(HCO3−) thermal waters originate from meteoric waters infiltrating SW of the study area, at elevation > 800 m a.s.l., circulating within both the Triassic evaporites and the overlying Miocene turbiditic formations, where salt dissolution/precipitation, sulfate reduction, and production of thermogenic CH4 occur. The equilibrium temperature of the deep fluid source is ~ 170 °C, corresponding to > 5 km depth. Cold springs are Ca2+–HCO3− type and show low amounts of biogenic CO2 and CH4 with no inputs of deep-originated fluids excepting in the immediate surroundings of the thermal area, confirming the lack of significant hydraulic connection between shallow and deep aquifers. We propose a genetic link between the quartz-hosted paleofluid and the thermal waters present in the area.